Hi

Since I haven't found any tool that does it I will try to do myself a small script that convert the wgsim output (indels) to a VCF file.

Before starting I'd like some confirmations on the way to proceed.

If wgsim simulation output the following variants:

20      74397   GCTTG   -       -
20      86509   -       TCTT    +

The first line is a deletion of GCTTG and the second line is an insert of TCTT. Since at positions 74396 and 86509 of my reference genome there are respectively nucleotides T and C, I can write the corresponding VCF:

#CHROM  POS     ID      REF     ALT     QUAL    FILTER  INFO    FORMAT  SAMPLE
20      74396   .       TGCTTG  T       .       .       .       .       .
20      86509   .       C       CTCTT   .       .       .       .       .

Is that correct? (I have serious doubt about the insertion and its correct position, 86508 or 86509)

Thank you. Pascal